Genome evolution mediated by Ty elements in &lt;i&gt;Saccharomyces&lt;/i&gt;

Dj, Garfinkel

doi:10.1159/000084939

Cited by 61 publications

(58 citation statements)

References 110 publications

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“…Yeast genes are under the control of endogenous Ty1 elements. There are two yeast genes transcribed by RNA polymerase II, ESF1 and NDJ1, which are naturally located in proximity to full-length endogenous Ty1 elements, in a configuration similar to that of the Ty1-his3⌬4 allele and the Ty1-TDH3-lacZ construct (22). With ESF1, this study provides the first example of a yeast gene naturally under the control of an endogenous Ty1 insertion.…”

Section: Discussionmentioning

confidence: 98%

Remodeling Yeast Gene Transcription by Activating the Ty1 Long Terminal Repeat Retrotransposon under Severe Adenine Deficiency

Servant

Pennetier

Lesage

2008

Molecular and Cellular Biology

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The Ty1 long terminal repeat (LTR) retrotransposon of Saccharomyces cerevisiae is a powerful model to understand the activation of transposable elements by stress and their impact on genome expression. We previously discovered that Ty1 transcription is activated under conditions of severe adenine starvation. The mechanism of activation is independent of the Bas1 transcriptional activator of the de novo AMP biosynthesis pathway and probably involves chromatin remodeling at the Ty1 promoter. Here, we show that the 5 LTR has a weak transcriptional activity and is sufficient for the activation by severe adenine starvation. Furthermore, we demonstrate that Ty1 insertions that bring Ty1 promoter sequences into the vicinity of a reporter gene confer adenine starvation regulation on it. We provide evidence that similar coactivation of genes adjacent to Ty1 sequences occurs naturally in the yeast genome, indicating that Ty1 insertions can mediate transcriptional control of yeast gene expression under conditions of severe adenine starvation. Finally, the transcription pattern of genes adjacent to Ty1 insertions suggests that severe adenine starvation facilitates the initiation of transcription at alternative sites, partly located in the 5 LTR. We propose that Ty1-driven transcription of coding and noncoding sequences could regulate yeast gene expression in response to stress.

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Section: Discussionmentioning

confidence: 98%

Remodeling Yeast Gene Transcription by Activating the Ty1 Long Terminal Repeat Retrotransposon under Severe Adenine Deficiency

Servant

Pennetier

Lesage

2008

Molecular and Cellular Biology

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“…It would be interesting to determine whether under the highly efficient homology-driven repair of D. radiodurans there is a similar capability for the generation of genome rearrangements. Chromosomal rearrangements between repetitive DNA sequences have been observed in a variety of laboratory and natural populations (12,21,(29)(30)(31). Although some CAs are selectively advantageous, there are also negative consequences to a mechanism that generates high rates of CAs.…”

Section: Cgh-arraymentioning

confidence: 99%

Double-strand breaks associated with repetitive DNA can reshape the genome

Argueso

Westmoreland

Mieczkowski

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

232

222

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Ionizing radiation is an established source of chromosome aberrations (CAs). Although double-strand breaks (DSBs) are implicated in radiation-induced and other CAs, the underlying mechanisms are poorly understood. Here, we show that, although the vast majority of randomly induced DSBs in G 2 diploid yeast cells are repaired efficiently through homologous recombination (HR) between sister chromatids or homologous chromosomes, Ϸ2% of all DSBs give rise to CAs. Complete molecular analysis of the genome revealed that nearly all of the CAs resulted from HR between nonallelic repetitive elements, primarily Ty retrotransposons. Nonhomologous end-joining (NHEJ) accounted for few, if any, of the CAs. We conclude that only those DSBs that fall at the 3-5% of the genome composed of repetitive DNA elements are efficient at generating rearrangements with dispersed small repeats across the genome, whereas DSBs in unique sequences are confined to recombinational repair between the large regions of homology contained in sister chromatids or homologous chromosomes. Because repeatassociated DSBs can efficiently lead to CAs and reshape the genome, they could be a rich source of evolutionary change.ectopic recombination ͉ gamma radiation ͉ genome rearrangements ͉ nonallelic homologous recombination ͉ retrotransposon

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“…In order to further assess the relationship between serial repitching and genetic variability, RFLP and RAPD-PCR were performed to analyse Ty elements and DNA regions between ␦ sequences, respectively. The analysis of Ty elements has been demonstrated to be a useful technique for the detection of genetic variants 53 , due partly to the high frequency of changes which can occur around Ty regions 10,17 and also to Ty-driven chromosomal translocations within the genome 41 . RAPD-PCR analysis of ␦ regions is known to be a valuable tool in differentiating sensu stricto yeast strains 28,32 as well as offering an indication of larger changes within the genome.…”

Section: Long Term Serial Repitching and The Genetic Integrity Of Brementioning

confidence: 99%

Long Term Serial Repitching and the Genetic and Phenotypic Stability of Brewer's Yeast

Powell

Diacetis²

2007

Journal of the Institute of Brewing

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Two brewing yeast strains, one employed for the production of an ale type product and the other used solely for bottle conditioning, were serially repitched over a period of one year. Subsequently each yeast culture was compared to the original stocks for a variety of phenotypic and genotypic characteristics. Fermentation performance was assessed in terms of flocculation capacity and the time required to achieve attenuation in 150 barrel fermentation vessels, while the propensity for the population to accumulate variants was assessed by analysing giant colony morphology. Changes to the genome were monitored by DNA fingerprinting of each yeast culture using RAPD-PCR and RFLP. Although some colony morphology variation was observed between fresh and old ale yeast cultures, there were no detectable genetic changes or alterations in fermentation characteristics to either yeast strain over the course of serial repitching. It is suggested that although some brewing yeast strains are susceptible to genetic drift, others are more resilient and can remain stable over extended periods of time. The propensity to produce variants may therefore play a significant role in determining the number of times a strain may be serially repitched, or its suitability for beer fermentations.

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Genome evolution mediated by Ty elements in <i>Saccharomyces</i>

Cited by 61 publications

References 110 publications

Remodeling Yeast Gene Transcription by Activating the Ty1 Long Terminal Repeat Retrotransposon under Severe Adenine Deficiency

Remodeling Yeast Gene Transcription by Activating the Ty1 Long Terminal Repeat Retrotransposon under Severe Adenine Deficiency

Double-strand breaks associated with repetitive DNA can reshape the genome

Long Term Serial Repitching and the Genetic and Phenotypic Stability of Brewer's Yeast

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